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It is well known that complex quaternion analysis plays an important role in the study of higher order boundary value problems of mathematical physics. Following the ideas given for real quaternion analysis, the paper deals with certain orthogonal decompositions of the complex quaternion Hilbert space into its subspaces of null solutions of Dirac type operator with an arbitrary complex potential. We then apply them to consider related boundary value problems, and to prove the existence and uniqueness as well as the explicit representation formulae of the underlying solutions.